Atlantis¶
Atlantis is a platform for designing, running, and analyzing biological simulations — from whole-cell E. coli models to composable process-bigraph workflows using COPASI, Tellurium, v2ecoli, and more.
You interact with Atlantis through one of three client applications — each exposes the same end-to-end workflow (build a simulator, run a simulation, download results) in a different format:
CLI |
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Command-line interface (fastest for scripting) |
TUI |
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Interactive terminal UI with sidebar navigation |
Web GUI |
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Marimo notebook UI (opens in browser) |
Getting Started
User Guide
- End-to-End Workflow
- Running a Sensitivity Campaign on AWS
- Prerequisites
- Step 1 — Authenticate to AWS
- Step 1b — Open a tunnel (GovCloud / internal-ALB deployments only)
- Step 2 — Set up ecoli-sources siblings
- Step 3 — Author a campaign spec
- Step 4 — Generate the Nextflow config
- Step 5 — Commit and push the vEcoli branch
- Step 6 — Build the simulator
- Step 7 — Launch the workflow with custom sources
- Step 8 — Download results
- Troubleshooting
- See also
- Choosing a Client Application
- CLI Reference
- Analysis Data Filtering
Compose Subsystem
Reference
Architecture (Internal)
- Architecture Overview
- AWS S3 Setup for SMS API
- Qumulo S3 Storage Setup Guide
- AWS Batch Workflow Architecture Analysis
- Table of Contents
- Constraints
- 1. Repository Findings
- 2. Current Architecture Summary
- 3. Existing CDK Infrastructure
- 4. Option A: Kubernetes Job per Workflow Run (Recommended)
- 5. Option B: Pet EC2 Launcher Service
- 6. Testability Comparison
- 7. Recommendation
- 8. Detailed Implementation Plan
- 9. Open Questions / Assumptions
- 10. Current Status and Next Steps
- Prior Art
- Multi-Arch Build Pipeline — AWS Batch with Docker-outside-of-Docker (DooD)